Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeBuffer

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    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub));
   
    LandscapeBuffer lbb= new BedGraphBuffer(f);
    String[] chrs= lbb.getUnsortedChromosomeList();
    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            int v= (int) (val-thr);
            if(v>0 ){
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public static void toDiff(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round( (v- refv) * 1000)/1000  );
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    String org= "refGene_hg19";
    //File f= new File(d+"/H9_H2A.Z.bar");
    File f= new File(d+"/H9_H3K56ac.bar");
    LandscapeBuffer lb= new BarReader(f);
   
   
    File od= new File(d+"/"+FileName.getBaseName(f));
    ScoreChipGene sc= new ScoreChipGene(lb, org, od, FileName.getBaseName(f));
   
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    String samp= "742";
   
   
    File datf= new File(dir+"/data/chip-seq/norm/norm_"+samp+".wig");
    LandscapeBuffer lb= new BedGraphReader(datf).getLandscapeBuilder();
   
   
   
    AntisenseFraction aa= new AntisenseFraction(f, lb);
   
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    File f= new File("out/score/set/sacCer1-xu/scan/intra_300_0_10_51.bed");
   
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
   
    String s= "884-rrp6d-wt";
    LandscapeBuffer lbf= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_for.wig"));
    LandscapeBuffer lbr= new BedGraphBuffer(new File(fd+"/"+s+"_sacCer1_rev.wig"));
    System.out.println(1);
   
    LinkAntisense ll= new LinkAntisense(gb, lbf, lbr);
    //LinkAntisense ll= new LinkAntisense(gb, null, null);
    ll.writeToFile(new File("out/score/set/sacCer1-xu/scan/linkAnti_"+FileName.getBaseName(f) +".bed"));
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    }
    */
   
   
   
    LandscapeBuffer lbf= new BedGraphBuffer(f);
    LandscapeBuffer lbi= new BedGraphBuffer(in);
    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub));
   
    String[] chrs= lbf.getUnsortedChromosomeList();
    for( int i=0; i<chrs.length; i++ ){
        LandscapeBuilder lbout= new LandscapeBuilder();
        String chr= chrs[i];
        System.out.print(chr+"  ");
        ArrayList<Region> frs= lbf.getLandscape2DForChromosome(chr).getRegions();
        ArrayList<Region> irs= lbi.getLandscape2DForChromosome(chr).getRegions();
        RegionBuffer buf= new RegionBuffer(irs);
        for( int j=0; j<frs.size(); j++ ){
            Region fr= frs.get(j);
            ArrayList<Region> bufrs= buf.reloadAndGetList(fr);
            double ival= RegionBuffer.getOverlap(bufrs, fr) / (fr.getRange()+1);
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    System.out.println("med: "+ med+"   sd: "+ sd+"     "+ thr);

    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub2));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub2));
   
    LandscapeBuffer lbb= new BedGraphBuffer(f);
    String[] chrs= lbb.getUnsortedChromosomeList();
    for( int k=0; k<chrs.length ; k++ ){
        String chr = chrs[k];
        System.out.print(chr+"  ");
        ArrayList<Region> rs= lbb.getLandscape2DForChromosome(chr).getRegions();
        for( int i=1; i<rs.size() ; i++ ){
            Region r= rs.get(i);
            double val= Double.parseDouble(r.attribute().toString());
            if(val>thr){
                double v= val-thr;
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    new BedGraphExporter(tr.toLandscapeBuilder(), tit).writeToFile(out);
}
   
   
public static void unlog(File wig, File out, String tit) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(wig);
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    BedGraphExporter.writeTitle(bw, tit);
    String[] chrs= lb.getUnsortedChromosomeList();
    for( int i=0; i<chrs.length ; i++ ){
        String chr= chrs[i];
        LandscapeBuilder lbt= new LandscapeBuilder();
        lbt.addAll(chr, lb.getLandscape2DForChromosome(chr));
        new LandscapeTransformer(lbt).unlog(Math.E);
        BedGraphExporter be= new BedGraphExporter(lbt);
        be.appendToFile(bw);
    }
    bw.close();
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public void writeToFile(File out)throws Exception{
    out.getParentFile().mkdirs();
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                if(refv<0.01){
                    refv=0.01;
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    be.writeToFile(of);
}
   

public static void toRatio(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round(v/refv * 1000)/1000  );
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Related Classes of fork.lib.bio.anno.genomic.LandscapeBuffer

  • data.cerevisiae.inhouse.a_norm.NormChipChipSignal
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
  • data.cerevisiae.lee2007.NormToLee
  • data.cerevisiae.nihroadmap.Score
  • data.cerevisiae.region.scan.AntisenseFraction
  • data.cerevisiae.region.scan.LinkAntisense
  • data.cerevisiae.region.scan.ScanIntra
  • data.cerevisiae.test.ratio.ToRatio
  • data.human.inhouse.norm.NormChipSeq
  • data.human.statham2014mods.NormTest
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